Do puppies goe through a fearful stage?

I have a 5 month old Border collie/australian shepherd mix puppy. She is a great dog besides this fearful stuff that has escalated in the past month. I was looking up about it and some people have expierienced the same thing especially with Border collies or mixes. She has taken to barking at dogs and even people she lives with if she sees them on the street. She will be 4 feet away from my brother and will conntinue to bark very aggressively and loudly even though she knows who he is. Will bark like crazy at other dogs. She gets lots of excercise but has been making it really embarrassing to even walk her around the block. I can't get her to stop barking unless I hold her muzzle shut. I have tried standing in front of her and telling her no and yanking the leash. Help? She is skittish of weird objects too. I really hope this is only a phase. She is awesome and is very well trained except for how skittish she is on walks! She was raised around tons of people, children cats and another dog. I do not understand why she is doing this.